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- PDB-4yn7: Non-oxidized YfiR -

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Basic information

Entry
Database: PDB / ID: 4yn7
TitleNon-oxidized YfiR
ComponentsYfiR
KeywordsTRANSCRIPTION / Periplasmic Repressor Protein / non-oxidized form
Function / homologyYfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / Negative regulator YfiR
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsYang, X. / Jiang, T.
Funding support China, 1items
OrganizationGrant numberCountry
the Strategic Priority Research ProgramXDB08010301 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structures of YfiR from Pseudomonas aeruginosa in two redox states
Authors: Yang, X. / Yang, X.-A. / Xu, M. / Zhou, L. / Fan, Z. / Jiang, T.
History
DepositionMar 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YfiR
B: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1654
Polymers34,9732
Non-polymers1922
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-44 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.725, 120.725, 87.457
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YfiR


Mass: 17486.574 Da / Num. of mol.: 2 / Fragment: UNP residues 35-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiR, PA1121 / Plasmid: pETDuet-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9I4L4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.71 Å3/Da / Density % sol: 73.87 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97889 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20544 / % possible obs: 99.9 % / Redundancy: 28.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.069 / Net I/av σ(I): 37.511 / Net I/σ(I): 13 / Num. measured all: 581053
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.6428.80.4979880.965100
2.64-2.6928.90.41210010.991100
2.69-2.7428.90.35710180.99100
2.74-2.8290.28910040.991100
2.8-2.8629.10.25310110.996100
2.86-2.93290.23610210.989100
2.93-329.10.19310010.994100
3-3.0829.10.1599930.991100
3.08-3.17290.1410351.001100
3.17-3.28290.11710021.007100
3.28-3.39290.10410341.054100
3.39-3.5328.90.09710061.102100
3.53-3.6928.80.110291.241100
3.69-3.8828.70.10310331.487100
3.88-4.1328.40.110141.58100
4.13-4.4527.80.09610441.653100
4.45-4.8927.20.08210521.258100
4.89-5.626.90.0610470.788100
5.6-7.0527.70.0510720.648100
7.05-5023.40.04211390.61897.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→49.679 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1030 5.12 %0
Rwork0.1894 19069 --
obs0.1916 20099 97.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.94 Å2 / Biso mean: 32.4137 Å2 / Biso min: 9.64 Å2
Refinement stepCycle: final / Resolution: 2.6→49.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 10 165 2494
Biso mean--34.63 35.83 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132366
X-RAY DIFFRACTIONf_angle_d1.2393203
X-RAY DIFFRACTIONf_chiral_restr0.08366
X-RAY DIFFRACTIONf_plane_restr0.005422
X-RAY DIFFRACTIONf_dihedral_angle_d14.025889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5961-2.73290.30361290.22782385251488
2.7329-2.90410.26651560.22562676283299
2.9041-3.12830.28951560.215327362892100
3.1283-3.44310.22371540.191927342888100
3.4431-3.94110.20361560.171327752931100
3.9411-4.96470.1941390.156528172956100
4.9647-49.68770.23941400.1952946308699

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